Deleting old boot record

Okay I'll try to make this as clear as possible. My machine has 3 physical disks - the first is the main disk and contains my vista installation. The second contains an install of Windows 7 which I don't really use at all. The third is an OS-less 1 TB storage drive with all my media, music, backups, etc. Today I had to reinstall Vista because of chronic instability that I attributed to corrupted system files. Well, I forgot how badly Vista f's up its own installs and did not remember to disable my other two disks before running the installer. Sure enough, it screwed something up and installed it's Boot, System Volume Information folders, and bootmgr file onto the 1 TB storage drive. Long story short, I fixed the boot settings to where both Vista and W7 boot properly, and the MBR is now located on the Vista C: drive, as it should be. However, the old boot files are still on my storage drive.

Now, granted, these files don't cause me any problems and I wouldn't ever even see them since they are hidden and protected system files, but they are there and for whatever reason annoying me. My question is how I would go about deleting them from the storage drive so that it contains nothing but my media and backups. For whatever reason, something is still accessing those files because I cannot delete them (it either says that access or denied or that the files are in use by another process). Additionally, setting the owner of those files as my Vista user account and giving myself full permissions doesn't do anything. I would like to get rid of them and keep only one MBR. The only thing I'm worried about now is whether or not they are necessary as, like I said, they are still being accessed by something. Does that mean it would screw up my boot settings if I deleted them? It doesn't make sense to me why Vista would utilize two separate boot records, especially when the latter is stored on a completely separate storage drive.

Any feedback is greatly appreciated! Thank you!
Hi Devil, welcome to NST.
Check in disk management that the "system" flag is not still on the data disk.
If your repair went as you intended, Vista should now be marked "system" "active" and "boot".
The easiest way to get rid of over-protected redundant Windows files, is not to use Windows.
Download and burn this Ubuntu live distro to a CD.
Boot the CD using the 1st "don't alter my PC" option and run Ubuntu directly from the CD.
Access the Data HDD and delete the /boot folder and the bootmgr
Don't touch the system volume information folder. That's nothing to do with the boot
Thanks for the reply. Yes, in the disk management the storage drive no longer has the system flag. Both it and the W7 disk are listed as active, primary partition. Only the Vista disk has system, boot, page file, etc flags. I will try deleting the files with Ubuntu later on, and report back. Hopefully, like I said, this does not alter vista booting in any way. In theory, it absolutely should not, but then again, Vista has its own way of doing things. I will post back my results.
I have a somewhat similar problem. I fear the MBR is residing on my drive D where Vista files are on drive C, however, drive D is designated as Drive 0 and drive C is designated as Drive 1. All screwed up!! so how can I remove the MBR from drive D and ploace it on drive C so that drive D can be removed while Vista still boots?